[Feature] BG-V1: `cellfinder-core` and `napari` merge

[willGraham01]

cellfinder-core and cellfinder-napari merge

Subtask of #33 | Depends on #45

A complete list of changes that need to be staged for the merging of cellfinder-core and cellfinder-napari into the existing cellfinder repository.

The existing cellfinder repo will have been migrated to workflows by #45, so we will be rm-ing the history of main with this update!

cellfinder-core

• [x] Update with "final version" release. Stage as a PR against main. https://github.com/brainglobe/cellfinder-core/pull/226
  • [x] Point users to cellfinder repository as replacement
  • [x] Point users to the blog post for more information
  • [x] Tagged version should be =v1.0.0 so that users can revert to old version easily, if they wish
  • [x] Push to PyPI
• [x] Depreciate package on PyPI
• [x] Migrate issues to cellfinder repo
• [x] Archive repository

cellfinder-napari

• [x] Update with "final version" release. Stage as a PR against main. https://github.com/brainglobe/cellfinder-napari/pull/177
  • [x] Point users to cellfinder repository as replacement
  • [x] Point users to the blog post for more information
  • [x] Tagged version should be =v1.0.0 so that users can revert to old version easily, if they wish
  • [x] Push to PyPI
• [x] Depreciate package on PyPI
• [x] Migrate issues to cellfinder repo
• [x] Archive repository

cellfinder

• [x] Create dev branch for pulling-in of cellfinder-core and cellfinder-napari: https://github.com/brainglobe/cellfinder/tree/dev-bg-v2 is the branch with the merged versions of cellfinder-core and cellfinder-napari.
  • [x] Add a CLI alias for "cellfinder" that tells users to install BG-workflows and use the updated name.
  • [x] Ensure headless display fix is incorporated into dev branch
  • [x] This will need to be a clean branch, with no related history to main
  • [x] It should be this branch which will need to be pulled from cellfinder-core
  • [x] There will be two submodules, core and napari, that perform analogous functions to the previous separate repositories
  • [x] napari-hub preview workflow to be binned: https://github.com/brainglobe/cellfinder/pull/251
  • [x] Package metadata needs updating
  • [x] The two READMEs from cellfinder-napari and cellfinder-core need to be reconciled
  • [x] The badges and pins should update to point to the cellfinder repo on PyPI
  • [x] Move appropriate README content to the documentation website
• [x] Move current main branch to cellfinder-pre-brainglobe-v1. Lock the branch if possible, and no longer make it default.
• [x] Move dev branch to main, and setup the appropriate CI checks and protection rules. Adjust the workflows if not done automatically.
• [x] Publish v1.0 release to PyPI ASAP, from the "new main" branch
• [x] https://github.com/brainglobe/cellfinder/pull/347
• [x] Re-in CI checks once brainglobe-workflows update goes in

brainglobe/website

• [x] Merge in when ready: https://github.com/brainglobe/brainglobe.github.io/pull/104
• [x] Accomodate cellfinder CLI renaming to brainmapper as per Zulip chat.
• [x] Blog post
• [x] Update v1 release changelog
• [x] Update install guidelines
  • [x] Recommended install is pip into a clean venv/conda env etc.
  • [x] MacOS M1 users have issues with napari, which will require some additional instructions
• [x] Update developer / contributing docs
• [x] Update tool documentation - will need to move core and napari info into a single place

brainglobe-workflows

• [x] cellfinder-core/napari text in README to be updated
• [x] Package to depend on cellfinder version >=1 again
• [x] API needs to switch from cellfinder-core to cellfinder.core etc
• [x] Accomodate cellfinder CLI renaming to brainmapper as per Zulip chat.
• [x] https://github.com/brainglobe/brainglobe-workflows/pull/54 <- merge when cellfinder new version is released and CI passes!
• [x] Release new version v1.1.0 to PyPI

[willGraham01]

Closing as completed with the migration on 2024-01-03.